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Capwire calculates 95% CIs using the parametric bootstrap [27].
Matrices were generated using the parametric bootstrap approach outlined in Supplemental Text S1.
First, we estimated means and confidence intervals for λ and stable stage distributions for the Isolated tributary using the parametric bootstrap approach outlined in Supplemental Text S1.
Cyt b mismatch distributions and raggedness index (r) [ 99] were calculated by clade in ARLEQUIN under a model of sudden expansion using the parametric bootstrap approach (α = 0.05; 1000 bootstraps) [ 100].
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When the single observation is composed of numerous components, as a network is composed of nodes and links, we can use the parametric bootstrap to assemble bootstrap networks by resampling from the components.
The branch robustness of ML trees was estimated using the non parametric bootstrap procedure (100 replicates of the original alignment) implemented in Treefinder with the same parameters than for ML tree inference.
To calculate confidence intervals for the reproductive number we use an approximation of the parametric bootstrap percentile interval method [21].
In the following, standard deviations given refer to the parametric bootstrap using only the original topology for calculating dates.
The parametric bootstrap uses our equations for the variation in the estimates of distances to simulate genetic distances including sampling and evolutionary variation.
The classical bootstrap is used to generate error bars for the MLEs obtained from the real data, and the parametric bootstrap is used to generate simulated replicates of the distribution of S. The distributions of selective coefficients for nonsynonymous mutations for three parametric bootstrap data sets are compared with the results for the real data in Figure 5.
In addition, confidence intervals of ICER were also estimated using the non-parametric bootstrap method [ 14].
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